Liftoff: accurate mapping of gene annotations
Liftoff: accurate mapping of gene annotations
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DOI：
10.1093/bioinformatics/btaa1016
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发表时间：
2021-06-15
期刊：
影响因子：
5.8
通讯作者：
Salzberg, Steven L.
中科院分区：
文献类型：
--
作者：
Shumate, Alaina;Salzberg, Steven L.
动机：DNA测序技术和计算方法的改进导致许多物种的高质量基因组组装的创建大幅增加。要了解这些基因组的生物学，注释的基因功能和其他功能元素是必不可少的，然而，对于大多数物种，只有参考基因组是很好的annotated.Results：一种策略，注释新的或改进的基因组组件是映射或“解除”的基因从以前注释的参考基因组。在这里，我们描述了Liftoff，一种新的基因组注释提升工具，能够在相同或密切相关的物种的两个组件之间映射基因。Liftoff将参考基因组中的基因与靶基因组进行比对，并找到最大化序列同一性的映射，同时保留每个外显子，转录本和基因的结构。我们表明，Liftoff可以准确地在两个版本的人类参考基因组之间定位99.9%的基因，平均序列同一性> 99.9%。我们还表明，Liftoff可以通过成功地将超过98.3%的人类蛋白质编码基因提升到具有98.2%序列同一性的黑猩猩基因组组装中来绘制跨物种基因。
Motivation: Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however, for most species, only the reference genome is well-annotated.Results: One strategy to annotate new or improved genome assemblies is to map or 'lift over' the genes from a previously annotated reference genome. Here, we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity >99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.3% of human protein-coding genes to a chimpanzee genome assembly with 98.2% sequence identity.